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ATP_mCNN: Predicting ATP binding sites through pretrained language models and multi-window neural networks

computers in Biology and Medicine 2025年 185卷 109541-109541页

作者： Le, Van-The Malik, Muhammad-Shahid Lin, Yi-Jing Liu, Yu-Chen Chang, Yan-Yun Ou, Yu-Yen Department of Computer Science and Engineering Yuan Ze University Chung-Li32003 Taiwan Graduate Program in Biomedical Informatics Yuan Ze University Chung-Li32003 Taiwan Department of Computer Sciences Karakoram International University Gilgit-Baltistan 15100 Pakistan

Adenosine triphosphate plays a vital role in providing energy and enabling key cellular processes through interactions with binding proteins. The increasing amount of protein sequence data necessitates computational methods for identifying binding sites. However, experimental identification of adenosine triphosphate-binding residues remains challenging. To address the challenge, we developed a multi-window convolutional neural network architecture taking pre-trained protein language model embeddings as input features. In particular, multiple parallel convolutional layers scan for motifs localized to different window sizes. Max pooling extracts salient features concatenated across windows into a final multi-scale representation for residue-level classification. On benchmark datasets, our model achieves an area under the ROC curve of 0.95, significantly improving on prior sequence-based models and outperforming convolutional neural network baselines. This demonstrates the utility of pre-trained language models and multi-window convolutional neural networks for advanced sequence-based prediction of adenosine triphosphate-binding residues. Our approach provides a promising new direction for elucidating binding mechanisms and interactions from primary structure. © 2024 Elsevier Ltd

关键词： Convolutional neural networks

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Chiral exceptional point enhanced active tuning and non reciprocity in micro-resonators

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光：科学与应用（英文版） 2025年第2期14卷 401-410页

作者： Hwaseob Lee Lorry Chang Ali Kecebas Dun Mao Yahui Xiao Tiantian Li Andrea Alù Sahin K.Özdemir Tingyi Gu Department of Electrical and Computer Engineering University of DelawareNewarkDelaware 19716USA Department of Engineering Science and Mechanics Pennsylvania State UniversityUniversity ParkPA 16802USA Photonics Initiative Advanced Science Research CenterCity University of New YorkNew YorkNY 10031USA Physics Program Graduate CenterCity University of New YorkNew YorkNY 10016USA Department of Engineering Science and Mechanics Pennsylvania State UniversityUniversity ParkPA 16802USA Department of Electrical and Computer Engineering Saint Louis UniversitySaint LouisMO 63103USA

Exceptional points(EPs)have been extensively explored in mechanical,acoustic,plasmonic,and photonic ***,little is known about the role of EPs in tailoring the dynamic tunability of optical devices.A specific type of EPs known as chiral EPs has recently attracted much attention for controlling the flow of light and for building sensors with better responsivity.A recently demonstrated route to chiral EPs via lithographically defined symmetric Mie scatterers on the rim of resonators has not only provided the much-needed mechanical stability for studying chiral EPs,but also helped reduce losses originating from nanofabrication imperfections,facilitating the in-situ study of chiral EPs and their contribution to the dynamics and tunability of ***,we use asymmetric Mie scatterers to break the rotational symmetry of a microresonator,to demonstrate deterministic thermal tuning across a chiral EP,and to demonstrate EP-mediated chiral optical nonlinear response and efficient electro-optic *** results indicate asymmetric electro-optic modulation with up to 17 dB contrast at GHz and CMOS-compatible voltage *** wafer-scale nano-manufacturing of chiral electro-optic modulators and the chiral EP-tailored tunning may facilitate new micro-resonator functionalities in quantum information processing,electromagnetic wave control,and optical interconnects.

关键词： active point micro chiral enhanced exceptional reciprocity resonators tuning

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MERNet: Multimodal Emotion Recognition in Conversation Network via Cross-Modal Knowledge Distillation and Contrastive Learning

MERNet: Multimodal Emotion Recognition in Conversation Netwo...

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International Conference on Big Data and Smart Computing (BIGCOMP)

作者： Sooyeon Hwang Gahgene Gweon Eunseong Kwon Interdisciplinary Program in Artificial Intelligence Seoul National University South Korea Graduate School of Convergence Science and Technology Seoul National University South Korea Dept. of Computer Science and Engineering POSTECH South Korea

ISBN: (数字)9798331529024

ISBN: (纸本)9798331529031

Multimodal Emotion Recognition in Conversation (ERC) is a task of predicting the emotion of each utterance in a conversation by utilizing both verbal and non-verbal modalities. However, existing approaches often struggle to bridge cross-modal gaps, resulting in misaligned features and frequent misclassification of minority emotions into semantically similar majority emotions. To address these challenges, we propose MERNet, a framework that employs cross-modal knowledge distillation and contrastive learning to align multimodal features and effectively distinguish subtle emotions in conversations. Our framework consists of two stages: 1) guiding non-verbal modalities with the text modality to transfer knowledge and align their features, and 2) applying contrastive learning with emotion labels as anchors to distinguish subtle differences between similar emotions and address the class imbalance problem. Experiments conducted on two benchmark datasets, IEMOCAP and MELD, demonstrate that our MERNet outperforms existing state-of-the-art models.

关键词： Knowledge engineering Bridges Emotion recognition Visualization Computational modeling Contrastive learning Benchmark testing Linguistics Big Data

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Dimensionality reduction in 3D causal deep learning for neuroimage generation: an evaluation study

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Journal of Medical Imaging 2025年第2期12卷

作者： Ohara, Erik Y. Vigneshwaran, Vibujithan Souza, Raissa Vamosi, Finn G. Wilms, Matthias Forkert, Nils D. University of Calgary Biomedical Engineering Graduate Program Calgary AB Canada University of Calgary Department of Radiology Calgary AB Canada University of Calgary Hotchkiss Brain Institute Calgary AB Canada University of Calgary Alberta Children's Hospital Research Institute Calgary AB Canada University of Calgary Department of Computer Science Calgary AB Canada University of Calgary Departments of Pediatrics and Community Health Sciences Calgary AB Canada

Purpose: Causal deep learning (DL) using normalizing flows allows the generation of true counterfactual images, which is relevant for many medical applications such as explainability of decisions, image harmonization, and in-silico studies. However, such models are computationally expensive when applied directly to high-resolution 3D images and, therefore, require image dimensionality reduction (DR) to efficiently process the data. The goal of this work was to compare how different DR methods affect counterfactual neuroimage generation. Approach: Five DR techniques [2D principal component analysis (PCA), 2.5D PCA, 3D PCA, autoencoder, and Vector Quantised-Variational AutoEncoder] were applied to 23,692 3D brain images to create low-dimensional representations for causal DL model training. Convolutional neural networks were used to quantitatively evaluate age and sex changes on the counterfactual neuroimages. Age alterations were measured using the mean absolute error (MAE), whereas sex changes were assessed via classification accuracy. Results: The 2.5D PCA technique achieved the lowest MAE of 4.16 when changing the age variable of an original image. When sex was changed, the autoencoder embedding led to the highest classification accuracy of 97.84% while also significantly impacting the age variable predictions, increasing the MAE to 5.24 years. Overall, 3D PCA provided the best balance, with an age prediction MAE of 4.57 years while maintaining 94.01% sex classification accuracy when altering the age variable and 94.73% sex classification accuracy and the lowest age prediction MAE (3.84 years) when altering the sex variable. Conclusions: 3D PCA appears to be the best-suited DR method for causal neuroimage analysis. © 2025 Society of Photo-Optical Instrumentation Engineers (SPIE).

关键词： causal artificial intelligence causality deep learning dimensionality reduction generative models normalizing flows

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Implementation and Evaluation of 0.6 µm CMOS Complex RCPF for Accurate Frequency Response Measurement

IEEJ Transactions on Electronics, Information and Systems

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IEEJ Transactions on Electronics, Information and Systems 2025年第1期145卷 25-37页

作者： Sato, Lina Fukagawa, Kanta Shouno, Kazuhiro Tanimoto, Hiroshi Muto, Cosy Moriyama, Seijiro Takahashi, Chikau Yoshino, Michitaka Graduate School of Science and Technology Degree Programs in Systems and Information Engineering Master’s Program in Computer Science University of Tsukuba Japan Division of Information Engineering University of Tsukuba 1-1-1 Tennoudai Ibaraki Tsukuba305-8573 Japan Kitami Institute of Technology 165 Koen-cho Hokkaido Kitami090-8507 Japan Faculty of Education Nagasaki University 1-14 Bunkyo-machi Nagasaki852-8521 Japan Anagix Corporation 3-22-27 Numama Kanagawa Zushi249-0004 Japan Takamori Corporation Japan Research Center for Micro-Nano Technology Hosei University 3-11-15 Midori-cho Koganei Tokyo184-0003 Japan

This paper describes the implementation and evaluation of an RC polyphase filter (RCPF) and circuitry for measuring its frequency characteristics. The integrated circuit is fabricated on a 0.6 µm CMOS process and its supply voltage is 5 V. The integrated circuit includes a filter under test (FUT), a four-phase square wave generator, several analog switches and differential amplifiers to amplify the high-impedance signals of the RCPF. This FUT is a third-order complex RCPF whose passband is 8 − 40 MHz. This paper describes the design of these circuits in detail. This integrated circuit can select two measurement methods by means of external control signals. The first method uses a four-phase square wave. The frequency characteristics are measured by using an on-chip four-phase square wave generator driven by an external clock generator and by a spectrum analyzer tuned to the fundamental frequency. The second method uses an external network analyzer. Furthermore, this integrated circuit is equipped with a calibration circuit to measure the frequency characteristics of the circuitry except FUT by passing through the input / output signals of the FUT. As a result, the frequency characteristics of the FUT itself can be accurately measured. The effectiveness is confirmed through evaluation of the fabricated integrated circuit. © 2025 The Institute of Electrical Engineers of Japan.

关键词： Differential amplifiers

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FDAM: Filter-Dedicated Approximate Multiplier Design for Real-Time CNN Acceleration

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IEEE Transactions on computer-Aided Design of Integrated Circuits and Systems 2025年

作者： Nguyen, Kihwan Kim Xuan Truong Jeon, Dongsuk Lee, Hyuk-Jae Korea Republic of program Department of Electrical Engineering Seoul08826 Korea Republic of Inter-University Semiconductor Research Center Seoul National University Graduate School of Convergence Science and Technology Research Institute for Convergence Science Seoul08826 Korea Republic of Department of Electrical and Computer Engineering Seoul08826 Korea Republic of

Video super-resolution (VSR) is widely used in various high-definition applications, such as HDTVs and smartphones, requiring a dedicated upscaling technique for realtime full-HD generation. To reduce on-chip buffers for largesize output feature maps, a streaming VSR accelerator may employ an output stationary dataflow, leading to a large energy consumption caused by frequent filter switching. To mitigate this, we introduce a new filter-dedicated multiplier design for realtime VSR acceleration. We replace costly multipliers with adders, shifters, and multiplexers (MUXes), referred to as unified multiple constant multiplications (UMCM). The conventional UMCM, however, may incur considerable area/power overhead due to the unified topology constraint among different filter sets. To address this problem, we propose a new approximated MCM (AMCM) problem to relax the constraint and an approximate compatible graph synthesis (A-CGS) framework to efficiently solve AMCM by jointly searching for approximated filters and constructing a unified graph. Additionally, we suggest a lightweight finetuning method by freezing approximated filters and only finetuning biases, which can recover the original model’s accuracy within a few epochs. Experimental results with synthetic data demonstrate that AMCM reduces the area by up to 49.8%, 44.8%, and 40.3% when considering constant sets of 2, 4, and 8, respectively. Our designs with SR application achieve up to a 73.3% reduction in energy consumption. Experiments with the Set5 and Set14 datasets show that our model with bias correction achieves similar restoration performance compared to the eightbit models. © 1982-2012 IEEE.

关键词： Acceleration

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Contract-Inspired Contest Theory for Controllable Image Generation in Mobile Edge Metaverse

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IEEE Transactions on Mobile Computing 2025年

作者： Liu, Guangyuan Du, Hongyang Wang, Jiacheng Niyato, Dusit Kim, Dong In Nanyang Technological University College of Computing and Data Science Energy Research Institute @ NTU Interdisciplinary Graduate Program Singapore University of Hong Kong Department of Electrical and Electronic Engineering Hong Kong Hong Kong Nanyang Technological University College of Computing and Data Science Singapore Sungkyunkwan University Department of Electrical and Computer Engineering Korea Republic of

The rapid advancement of immersive technologies has propelled the development of the Metaverse, where the convergence of virtual and physical realities necessitates the generation of high-quality, photorealistic images to enhance user experience. However, generating these images, especially through Generative Diffusion Models (GDMs), in mobile edge computing environments presents significant challenges due to the limited computing resources of edge devices and the dynamic nature of wireless networks. This paper proposes a novel framework that integrates contract-inspired contest theory, Deep Reinforcement Learning (DRL), and GDMs to optimize image generation in these resource-constrained environments. The framework addresses the critical challenges of resource allocation and semantic data transmission quality by incentivizing edge devices to efficiently transmit high-quality semantic data, which is essential for creating realistic and immersive images. The use of contest and contract theory ensures that edge devices are motivated to allocate resources effectively, while DRL dynamically adjusts to network conditions, optimizing the overall image generation process. Experimental results demonstrate that the proposed approach not only improves the quality of generated images but also achieves superior convergence speed and stability compared to traditional methods. This makes the framework particularly effective for optimizing complex resource allocation tasks in mobile edge Metaverse applications, offering enhanced performance and efficiency in creating immersive virtual environments. © 2002-2012 IEEE.

关键词： Resource allocation

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Effective Dimension Aware Fractional-Order Stochastic Gradient Descent for Convex Optimization Problems

arXiv

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arXiv 2025年

作者： Partohaghighi, Mohammad Marcia, Roummel Chen, YangQuan Electrical Engineering and Computer Science graduate program University of California Merced United States Department of Applied Mathematics University of California Merced MercedCA United States Lab Department of Mechanical Engineering School of Engineering University of California MercedCA95343 United States

Fractional-order stochastic gradient descent (FOSGD) leverages a fractional exponent to capture long-memory effects in optimization, yet its practical impact is often constrained by the difficulty of tuning and stabilizing this exponent. In this work, we introduce 2SED Fractional-Order Stochastic Gradient Descent (2SEDFOSGD), a novel method that synergistically combines the Two-Scale Effective Dimension (2SED) algorithm with FOSGD to automatically calibrate the fractional exponent in a data-driven manner. By continuously gauging model sensitivity and effective dimensionality, 2SED dynamically adjusts the exponent to curb erratic oscillations and enhance convergence rates. Theoretically, we demonstrate how this dimension-aware adaptation retains the benefits of fractional memory while averting the sluggish or unstable behaviors frequently observed in naive fractional SGD. Empirical evaluations across multiple benchmarks confirm that our 2SED-driven fractional exponent approach not only converges faster but also achieves more robust final performance, suggesting broad applicability for fractional-order methodologies in large-scale machine learning and related domains. © 2025, CC BY.

关键词： Convex optimization

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Enhanced Performance and Data Privacy in Lung Nodule Classification via Federated Deep Learning Approach 24

Enhanced Performance and Data Privacy in Lung Nodule Classif...

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2024 7th International Conference on Healthcare Service Management, ICHSM 2024

作者： Nguyen, Duc-Khanh Li, Ai-Hsien Adam Lai, Yen-Jun Chiu, Yen-Ling Phan, Dinh-Van Chien, Ting-Ying Chan, Chien-Lung Department of Information Management Yuan Ze University Taoyuan Taiwan Department of Statistics and Informatics University of Economics The University of Danang Danang Viet Nam Division of Cardiology Far Eastern Memorial Hospital New Taipei Taiwan Graduate Program in Biomedical Informatics Yuan Ze University Taoyuan Taiwan Department of Radiology Far Eastern Memorial Hospital New Taipei Taiwan Graduate Institute of Medicine and Graduate Program in Biomedical Informatics Yuan Ze University Taoyuan Taiwan Department of Medical Research Far Eastern Memorial Hospital New Taipei Taiwan Department of Computer Science and Engineering Yuan Ze University Taoyuan Taiwan ZDT Group- YZU Joint Research and Development Center for Big Data Taoyuan Taiwan Yuan Ze University Taoyuan Taiwan

ISBN: (纸本)9798400710162

This study explores the feasibility of deep learning for classifying nodule neoplasms, analyzing their performance on two openly available datasets, LUNGx SPIE, and LIDC-IDRI. These datasets offer valuable diversity in image quantity, quality, and malignancy annotation methodologies, posing a real-world challenge for effective model development. To handle the disparities in these diverse datasets, we aim to develop a robust classification model trained using federated learning. This decentralized approach allows model training across datasets without sharing patient data, preserving privacy and overcoming data fragmentation. Our experiments demonstrate that federated learning enables the development of a robust and superior deep learning model compared to individual models trained on limited data. This combination of deep learning, and federated learning holds immense promise for nodule neoplasm classification and can significantly improve patient care and outcomes. © 2024 Copyright held by the owner/author(s).

关键词： Federated learning

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Contract-Inspired Contest Theory for Controllable Image Generation in Mobile Edge Metaverse

arXiv

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arXiv 2025年

作者： Liu, Guangyuan Du, Hongyang Wang, Jiacheng Niyato, Dusit Kim, Dong In College of Computing and Data Science The Energy Research Institute @ NTU Interdisciplinary Graduate Program Nanyang Technological University Singapore Department of Electrical and Electronic Engineering University of Hong Kong Hong Kong College of Computing and Data Science Nanyang Technological University Singapore Department of Electrical and Computer Engineering Sungkyunkwan University Korea Republic of

关键词： Mobile edge computing

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